Stephen A. Harris

Chloroplast DNA and biosystematics: The effects of intraspecific diversity and plastid transmission

Summary Harris, S. A. & Ingram, R.: Chloroplast DNA and biosystematics: The effects of intraspecific diversity and plastid transmission. - Taxon 40: 393-412. 1991. - ISSN 0040-0262. The widespread application of chloroplast DNA (cpDNA) to plant biosystematics is usually based on a number of assumptions. The assumption of low levels of intraspecific cpDNA variation is reviewed and the conclusion reached that far from being rare, intraspecific cpDNA variation is relatively common. The evidence for the assumption of predominantly maternal plastid transmission is also reviewed. In both of the cases some of the possible effects on phylogenetic reconstruction are considered.

Genetic clues to the origin of the apple

Molecular genetic markers complement archaeological, breeding and geographical investigations of the origins, history and domestication of plants. With increasing access to wild apples from Central Asia, along with the use of molecular genetic markers capable of distinguishing between species, and explicit methods of phylogeny reconstruction, it is now possible to test hypotheses about the origin of the domesticated apple. Analyses of nuclear rDNA and chloroplast DNA (cpDNA) sequences indicate that the domesticated apple is most closely related to series Malus species. Moreover, the occurrence of a shared 18-bp duplication in the cpDNAs of wild and cultivated apple supports the close relationship between them. Hypotheses about the hybridization and the origin of the domesticated apple cannot be rejected completely until more variable, phylogenetically informative markers are found.

Radiocarbon-based chronology for dynastic Egypt.

Date with the Pharaohs Ancient Egypt dominated the Mediterranean world for several thousand years. However, the absolute chronology of this civilization has been uncertain, even though the sequence of rulers is well documented. Bronk Ramsey et al. (p. 1554; see the Perspective by Bruins) now provide a detailed radiocarbon-based record using more than 200 samples that spans much of this time and reduces uncertainties in some cases to less than 20 years. To avoid artifacts, the authors dated only short-lived plant remains from known contexts (i.e., that were associated with specific reigns). They then used the known reign lengths as a further constraint to obtain a final chronology. The final dates agree most closely with the previous older chronology but force some revisions to the timing of events in the Old Kingdom, the period in the third millennium B.C.E. when Egypt attained its first continuous peak of civilization. Many radiocarbon dates from short-lived plant remains provide a long and accurate chronology for ancient Egypt. The historical chronologies for dynastic Egypt are based on reign lengths inferred from written and archaeological evidence. These floating chronologies are linked to the absolute calendar by a few ancient astronomical observations, which remain a source of debate. We used 211 radiocarbon measurements made on samples from short-lived plants, together with a Bayesian model incorporating historical information on reign lengths, to produce a chronology for dynastic Egypt. A small offset (19 radiocarbon years older) in radiocarbon levels in the Nile Valley is probably a growing-season effect. Our radiocarbon data indicate that the New Kingdom started between 1570 and 1544 B.C.E., and the reign of Djoser in the Old Kingdom started between 2691 and 2625 B.C.E.; both cases are earlier than some previous historical estimates.

Suprageneric phylogenetics of Myrteae, the generically richest tribe in Myrtaceae (Myrtales)

To clarify relationships within the predominantly Neotropical and exclusively fleshy-fruited Myrteae (49 genera and c. 2,500 species), we provide a phylogenetic hypothesis for evolutionary relationships between 31 of these genera by analyzing nuclear ITS and ETS ribosomal DNA, and plastid psbA-trnH and matK DNA sequences from 75 Myrteae species and 13 outgroup taxa using parsimony and Bayesian inference. Four morphological characters are epitomized on the resulting trees, and biogeographical analyses are also performed. Myrteae are monophyletic, comprising seven clades plus two isolated taxa of unclear relationships. Morphological characters exhibit homoplasy, although in combination are useful for clade diagnosis. Biogeographical analyses are inconclusive regarding the ancestral area of the tribe, but South American colonization before northern radiation via the Andes appears likely. The largest genera, Eugenia and Myrcia s.1., have western and south-eastern South American origins, respectively.

Taxonomy of the genus Malus Mill. (Rosaceae) with emphasis on the cultivated apple, Malus domestica Borkh.

Abstract. Twenty-nine Malus species, 12 M. domestica cultivars and representative outgroup taxa were chosen for sequence analysis of the internal transcribed spacer of nuclear ribosomal DNA and the matK region of the chloroplast genome, in order to develop an explicit phylogenetic hypothesis for the genus and identify potential germplasm donors to the domesticated apple, M. domestica. Maximum parsimony analysis generated nuclear and chloroplast cladograms that provide reasonable resolution of sub-generic groups, as recognised in classifications. All of the close relatives of M. domestica occur in a poorly resolved series Malus clade. Two matK duplications were found, one in series Malus and the other in most M. domestica cultivars and one Central Asian M. sieversii accession.

Predicting unknown species numbers using discovery curves

A common approach to estimating the total number of extant species in a taxonomic group is to extrapolate from the temporal pattern of known species descriptions. A formal statistical approach to this problem is provided. The approach is applied to a number of global datasets for birds, ants, mosses, lycophytes, monilophytes (ferns and horsetails), gymnosperms and also to New World grasses and UK flowering plants. Overall, our results suggest that unless the inventory of a group is nearly complete, estimating the total number of species is associated with very large margins of error. The strong influence of unpredictable variations in the discovery process on species accumulation curves makes these data unreliable in estimating total species numbers.

Simple allelic-phenotype diversity and differentiation statistics for allopolyploids

The analysis of genetic diversity within and between populations is a routine task in the study of diploid organisms. However, population genetic studies of polyploid organisms have been hampered by difficulties associated with scoring and interpreting molecular data. This occurs because the presence of multiple alleles at each locus often precludes the measurement of genotype or allele frequencies. In allopolyploids, the problem is compounded because genetically distinct isoloci frequently share alleles. As a result, analysis of genetic diversity patterns in allopolyploids has tended to rely on the interpretation of phenotype frequencies, which loses information available from allele composition. Here, we propose the use of a simple allelic-phenotype diversity statistic (H′) that measures diversity as the average number of alleles by which pairs of individuals differ. This statistic can be extended to a population differentiation measure (F′ST), which is analogous to FST. We illustrate the behaviour of these statistics using coalescent computer simulations that show that F′ST behaves in a qualitatively similar way to FST, thus providing a useful way to quantify population differentiation in allopolyploid species.

Divergent and reticulate species relationships in Leucaena (Fabaceae) inferred from multiple data sources: insights into polyploid origins and nrDNA polymorphism

Previous analyses of species relationships and polyploid origins in the mimosoid legume genus Leucaena have used chloroplast DNA (cpDNA) restriction site data and morphology. Here we present an analysis of a new DNA sequence data set for the nuclear ribosomal DNA (nrDNA) 5.8S subunit and flanking ITS 1 and ITS 2 spacers, a simultaneous analysis of the morphology, ITS and cpDNA data sets for the diploid species, and a detailed comparison of the cpDNA and ITS gene trees, which include multiple accessions of all five tetraploid species. Significant new insights into species relationships and polyploid origins, including that of the economically important tropical forage tree L. leucocephala, are discussed. Heterogeneous ITS copy types, including 26 putative pseudogene sequences, were found within individuals of four of the five tetraploid and one diploid species. Potential pseudogenes were identified using two pairwise comparison approaches as well as a tree-based method that compares observed and expected proportions of total ITS variation contributed by the 5.8S subunit optimized onto branches of one of the ITS gene trees. Inclusion of putative pseudogene sequences in the analysis provided evidence that some pseudogenes in allopolyploid L. leucocephala are not the result of post-allopolyploidization gene silencing, but were inherited from its putative diploid maternal progenitor L. pulverulenta.

HYBRIDIZATION, POLYPLOIDY, AND THE EVOLUTION OF SEXUAL SYSTEMS IN MERCURIALIS (EUPHORBIACEAE)

Abstract Hybridization and polyploidy are widely believed to be important sources of evolutionary novelty in plant evolution. Both can lead to novel gene combinations and/or novel patterns of gene expression, which in turn provide the variation on which natural selection can act. Here, we use nuclear and plastid gene trees, in conjunction with morphological data and genome size measurements, to show that both processes have been important in shaping the evolution of the angiosperm genus Mercurialis, particularly a clade of annual lineages that shows exceptional variation in the sexual system. Our results indicate that hexaploid populations of M. annua, in which the rare sexual system androdioecy is common (the occurrence of males and hermaphrodites) is of allopolyploid origin involving hybridization between an autotetraploid lineage of M. annua and the related diploid species M. huetii. We discuss the possibility that androdioecy may have evolved as a result of hybridization between dioecious M. huetii and monoecious tetraploid M. annua, an event that brought together the genes for specialist males with those for hermaphrodites.

Potential of the 5′ and 3′ Ends of the Intergenic Spacer (IGS) of rDNA in the Cyperaceae: New Sequences for Lower‐Level Phylogenies in Sedges with an Example from Uncinia Pers.

In plants, the internal transcribed spacers (ITS; ca. 450 base pairs) of nuclear ribosomal DNA (rDNA) are the only well‐characterized nuclear sequences that are both easily amplified and appropriately variable for addressing relationships at lower taxonomic levels. In this study, we assess the utility of rDNA noncoding fragments from the external transcribed spacer 1 (ETS 1f) and from the 5′ end of the intergenic spacer ( \documentclass{aastex} \usepackage{amsbsy} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{bm} \usepackage{mathrsfs} \usepackage{pifont} \usepackage{stmaryrd} \usepackage{textcomp} \usepackage{portland,xspace} \usepackage{amsmath,amsxtra} \usepackage[OT2,OT1]{fontenc} \newcommand\cyr{ \renewcommand\rmdefault{wncyr} \renewcommand\sfdefault{wncyss} \renewcommand\encodingdefault{OT2} \normalfont \selectfont} \DeclareTextFontCommand{\textcyr}{\cyr} \pagestyle{empty} \DeclareMathSizes{10}{9}{7}{6} \begin{document} \landscape